Multiple sequence alignment - TraesCS6B01G308200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6B01G308200 chr6B 100.000 4036 0 0 1 4036 552240600 552244635 0.000000e+00 7454
1 TraesCS6B01G308200 chr6B 82.674 860 120 21 2259 3116 14635144 14634312 0.000000e+00 736
2 TraesCS6B01G308200 chr6D 92.227 1904 92 21 2108 3960 366537283 366539181 0.000000e+00 2645
3 TraesCS6B01G308200 chr6D 91.133 1421 67 23 1 1408 366534910 366536284 0.000000e+00 1871
4 TraesCS6B01G308200 chr6D 97.059 612 12 3 1475 2080 366536680 366537291 0.000000e+00 1026
5 TraesCS6B01G308200 chr6A 94.157 1489 52 14 706 2165 507089642 507091124 0.000000e+00 2235
6 TraesCS6B01G308200 chr6A 91.679 1382 85 20 2167 3524 507091368 507092743 0.000000e+00 1888
7 TraesCS6B01G308200 chr6A 87.408 683 43 24 1 669 507088985 507089638 0.000000e+00 745
8 TraesCS6B01G308200 chr6A 86.695 466 44 4 3582 4033 507092776 507093237 6.020000e-138 501
9 TraesCS6B01G308200 chr2A 81.860 860 128 18 2259 3116 733418299 733417466 0.000000e+00 699
10 TraesCS6B01G308200 chr5A 81.512 860 131 18 2259 3116 688482112 688482945 0.000000e+00 682
11 TraesCS6B01G308200 chr4A 81.301 861 123 27 2259 3116 577728351 577729176 0.000000e+00 664
12 TraesCS6B01G308200 chr4B 81.228 863 121 31 2259 3116 483094245 483093419 0.000000e+00 658


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G308200 chr6B 552240600 552244635 4035 False 7454.000000 7454 100.00000 1 4036 1 chr6B.!!$F1 4035
1 TraesCS6B01G308200 chr6B 14634312 14635144 832 True 736.000000 736 82.67400 2259 3116 1 chr6B.!!$R1 857
2 TraesCS6B01G308200 chr6D 366534910 366539181 4271 False 1847.333333 2645 93.47300 1 3960 3 chr6D.!!$F1 3959
3 TraesCS6B01G308200 chr6A 507088985 507093237 4252 False 1342.250000 2235 89.98475 1 4033 4 chr6A.!!$F1 4032
4 TraesCS6B01G308200 chr2A 733417466 733418299 833 True 699.000000 699 81.86000 2259 3116 1 chr2A.!!$R1 857
5 TraesCS6B01G308200 chr5A 688482112 688482945 833 False 682.000000 682 81.51200 2259 3116 1 chr5A.!!$F1 857
6 TraesCS6B01G308200 chr4A 577728351 577729176 825 False 664.000000 664 81.30100 2259 3116 1 chr4A.!!$F1 857
7 TraesCS6B01G308200 chr4B 483093419 483094245 826 True 658.000000 658 81.22800 2259 3116 1 chr4B.!!$R1 857

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
86 87 0.106918 TTTTCACAGACCGGGCAACT 60.107 50.000 11.69 0.00 0.00 3.16 F
114 115 0.323999 ATACCCCCTTTCAAACGGGC 60.324 55.000 0.00 0.00 39.34 6.13 F
198 201 0.466007 TGCTGAACAGGCTTGAAGCA 60.466 50.000 19.89 16.94 44.75 3.91 F
2076 2449 1.004080 CCCAGTGGTCAGTCTGCTG 60.004 63.158 8.74 0.00 43.87 4.41 F
2555 3196 0.307760 GTGACTTTTCACGCTGTGGG 59.692 55.000 8.46 0.00 42.86 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1964 2330 0.034616 AGGAGTCAGACAAGCAGCAC 59.965 55.0 2.66 0.0 0.00 4.40 R
2076 2449 1.909700 TCCAAGCATTCCCACAGAAC 58.090 50.0 0.00 0.0 37.29 3.01 R
2165 2784 2.957402 ACAGCTCCACCATCAAAAGA 57.043 45.0 0.00 0.0 0.00 2.52 R
2890 3533 0.610509 TGGCCCAGCTGCGATAAAAA 60.611 50.0 8.66 0.0 0.00 1.94 R
3743 4430 1.835483 GCCTGCACTGTCAACTGTCG 61.835 60.0 0.00 0.0 0.00 4.35 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 3.614616 GTGAGCTAGATTTTCACAGACCG 59.385 47.826 0.00 0.00 40.62 4.79
85 86 0.958822 ATTTTCACAGACCGGGCAAC 59.041 50.000 11.69 0.00 0.00 4.17
86 87 0.106918 TTTTCACAGACCGGGCAACT 60.107 50.000 11.69 0.00 0.00 3.16
92 93 1.534235 AGACCGGGCAACTCACTCT 60.534 57.895 11.69 0.00 0.00 3.24
97 98 2.835764 ACCGGGCAACTCACTCTTTATA 59.164 45.455 6.32 0.00 0.00 0.98
105 106 5.806734 GCAACTCACTCTTTATACCCCCTTT 60.807 44.000 0.00 0.00 0.00 3.11
106 107 5.695424 ACTCACTCTTTATACCCCCTTTC 57.305 43.478 0.00 0.00 0.00 2.62
107 108 5.098663 ACTCACTCTTTATACCCCCTTTCA 58.901 41.667 0.00 0.00 0.00 2.69
108 109 5.550403 ACTCACTCTTTATACCCCCTTTCAA 59.450 40.000 0.00 0.00 0.00 2.69
109 110 6.045106 ACTCACTCTTTATACCCCCTTTCAAA 59.955 38.462 0.00 0.00 0.00 2.69
110 111 6.243148 TCACTCTTTATACCCCCTTTCAAAC 58.757 40.000 0.00 0.00 0.00 2.93
111 112 5.123344 CACTCTTTATACCCCCTTTCAAACG 59.877 44.000 0.00 0.00 0.00 3.60
112 113 4.591929 TCTTTATACCCCCTTTCAAACGG 58.408 43.478 0.00 0.00 0.00 4.44
113 114 3.369242 TTATACCCCCTTTCAAACGGG 57.631 47.619 0.00 0.00 41.71 5.28
114 115 0.323999 ATACCCCCTTTCAAACGGGC 60.324 55.000 0.00 0.00 39.34 6.13
115 116 1.428718 TACCCCCTTTCAAACGGGCT 61.429 55.000 0.00 0.00 39.34 5.19
116 117 2.275380 CCCCCTTTCAAACGGGCTG 61.275 63.158 0.00 0.00 39.22 4.85
117 118 1.530655 CCCCTTTCAAACGGGCTGT 60.531 57.895 0.00 0.00 39.22 4.40
118 119 1.659794 CCCTTTCAAACGGGCTGTG 59.340 57.895 0.00 0.00 32.83 3.66
119 120 1.659794 CCTTTCAAACGGGCTGTGG 59.340 57.895 0.00 0.00 0.00 4.17
122 123 2.010582 TTTCAAACGGGCTGTGGTGC 62.011 55.000 0.00 0.00 0.00 5.01
148 151 1.048601 AGAGTCACCGCTGGAAAGAA 58.951 50.000 1.50 0.00 0.00 2.52
166 169 4.762289 AGAAAAGCCTATCGGTGATTCT 57.238 40.909 0.00 0.00 0.00 2.40
168 171 2.246719 AAGCCTATCGGTGATTCTGC 57.753 50.000 0.00 0.00 0.00 4.26
170 173 0.603975 GCCTATCGGTGATTCTGCCC 60.604 60.000 0.00 0.00 0.00 5.36
198 201 0.466007 TGCTGAACAGGCTTGAAGCA 60.466 50.000 19.89 16.94 44.75 3.91
215 219 2.405892 GCAAAATGCTGTTGTCGAGT 57.594 45.000 0.00 0.00 40.96 4.18
216 220 2.046313 GCAAAATGCTGTTGTCGAGTG 58.954 47.619 0.00 0.00 40.96 3.51
217 221 2.541588 GCAAAATGCTGTTGTCGAGTGT 60.542 45.455 0.00 0.00 40.96 3.55
303 308 4.568072 AGACCACATATGCCTTGTAACA 57.432 40.909 1.58 0.00 0.00 2.41
424 429 3.589288 GGGAATAAGTGAGCCCCATATCT 59.411 47.826 0.00 0.00 37.04 1.98
425 430 4.783227 GGGAATAAGTGAGCCCCATATCTA 59.217 45.833 0.00 0.00 37.04 1.98
426 431 5.430089 GGGAATAAGTGAGCCCCATATCTAT 59.570 44.000 0.00 0.00 37.04 1.98
427 432 6.408662 GGGAATAAGTGAGCCCCATATCTATC 60.409 46.154 0.00 0.00 37.04 2.08
474 479 3.668447 TCTTCAGGTTCATTGTCTCTGC 58.332 45.455 0.00 0.00 0.00 4.26
535 545 6.017400 ACAAGCTTTCATATCCAGTGTTTG 57.983 37.500 0.00 0.00 0.00 2.93
591 601 7.348080 AGGCTTTTTACTCCCTATATTTTGC 57.652 36.000 0.00 0.00 0.00 3.68
611 622 2.168313 GCCCCCATTTGTAATGGTGAAG 59.832 50.000 15.28 2.63 37.48 3.02
659 670 1.069049 CCTTTTTGACCCCAGTTGCAG 59.931 52.381 0.00 0.00 0.00 4.41
682 693 6.196538 CAGTGCAAGATTTTGATCGATCAATG 59.803 38.462 34.66 29.04 45.30 2.82
759 770 3.704566 TGCTACTAGTAATCACCACCTGG 59.295 47.826 3.76 0.00 42.17 4.45
910 934 2.802816 CTCTCTCGCCCATAAAAATCCG 59.197 50.000 0.00 0.00 0.00 4.18
948 972 1.098050 AATCCAAACTCGCTGCCATC 58.902 50.000 0.00 0.00 0.00 3.51
971 995 4.873129 TGATTCGCTCGCCTCGCC 62.873 66.667 0.00 0.00 0.00 5.54
972 996 4.577246 GATTCGCTCGCCTCGCCT 62.577 66.667 0.00 0.00 0.00 5.52
973 997 4.577246 ATTCGCTCGCCTCGCCTC 62.577 66.667 0.00 0.00 0.00 4.70
1033 1057 1.226916 ACGGCGACAAACACGTACA 60.227 52.632 16.62 0.00 37.85 2.90
1438 1480 2.121460 CCCCCTCCCCTTATCCCC 60.121 72.222 0.00 0.00 0.00 4.81
1464 1506 3.923461 CGATTCTGTTCAACCTCTCTCAC 59.077 47.826 0.00 0.00 0.00 3.51
1469 1511 5.087323 TCTGTTCAACCTCTCTCACCTAAT 58.913 41.667 0.00 0.00 0.00 1.73
1625 1990 1.336440 CAGATCTCCGTCATCTTCGCT 59.664 52.381 0.00 0.00 0.00 4.93
1964 2330 2.361757 TGCTGTGAATCCTTGTTGTTGG 59.638 45.455 0.00 0.00 0.00 3.77
2076 2449 1.004080 CCCAGTGGTCAGTCTGCTG 60.004 63.158 8.74 0.00 43.87 4.41
2084 2457 1.506493 GTCAGTCTGCTGTTCTGTGG 58.494 55.000 13.99 0.00 43.05 4.17
2147 2524 7.870954 TGTTTGTGATAAACAGAGAGATTACGT 59.129 33.333 3.28 0.00 40.74 3.57
2165 2784 8.098912 AGATTACGTGGTATTAAGTTTTCAGGT 58.901 33.333 0.00 0.00 0.00 4.00
2175 2794 9.626045 GTATTAAGTTTTCAGGTCTTTTGATGG 57.374 33.333 0.00 0.00 0.00 3.51
2241 2860 0.595310 GCGACAAGAGGATAGTCCGC 60.595 60.000 0.00 0.00 42.75 5.54
2404 3023 5.471556 TCTAGTTGTCCAACCGAAATACA 57.528 39.130 6.55 0.00 42.06 2.29
2540 3180 1.802960 CAAGAGTCAGTGGCATGTGAC 59.197 52.381 19.80 19.80 42.95 3.67
2555 3196 0.307760 GTGACTTTTCACGCTGTGGG 59.692 55.000 8.46 0.00 42.86 4.61
2577 3218 5.331902 GGTCGATTTGGTGTGACATATTTG 58.668 41.667 0.00 0.00 33.04 2.32
2641 3282 7.751732 TCAAGTGTCAATTAAGTATGATGCAC 58.248 34.615 0.00 0.00 0.00 4.57
2644 3285 6.540189 AGTGTCAATTAAGTATGATGCACTCC 59.460 38.462 0.00 0.00 0.00 3.85
2649 3290 0.465705 AGTATGATGCACTCCGTGGG 59.534 55.000 0.00 0.00 33.64 4.61
2671 3312 5.278022 GGGCTTTTAGCTGCATATACTGTTC 60.278 44.000 1.02 0.00 41.99 3.18
2716 3358 9.490663 GAGTATTTATGTATTGTTCAACTGTGC 57.509 33.333 0.00 0.00 0.00 4.57
2718 3360 9.277565 GTATTTATGTATTGTTCAACTGTGCTG 57.722 33.333 0.00 0.00 0.00 4.41
2721 3363 3.944650 TGTATTGTTCAACTGTGCTGTGT 59.055 39.130 0.00 0.00 0.00 3.72
2768 3410 2.504367 ACAAAAGTCAGCGCCTATGTT 58.496 42.857 2.29 0.00 0.00 2.71
2963 3608 0.668706 CGTGCCCTCAGACAGTGAAG 60.669 60.000 0.00 0.00 33.60 3.02
3118 3763 4.579869 ACAAATAATGTGGAGCGAGTTCT 58.420 39.130 0.00 0.00 41.93 3.01
3209 3854 1.798813 GATATTCATCCGTGCGGTTCC 59.201 52.381 10.60 0.00 36.47 3.62
3217 3862 0.675522 CCGTGCGGTTCCCTGTATTT 60.676 55.000 1.93 0.00 0.00 1.40
3231 3876 4.024556 CCCTGTATTTCGCTTCTAATGCTG 60.025 45.833 0.00 0.00 0.00 4.41
3242 3887 2.029623 TCTAATGCTGTAGACCGGTCC 58.970 52.381 30.82 17.09 0.00 4.46
3243 3888 0.742505 TAATGCTGTAGACCGGTCCG 59.257 55.000 30.82 17.29 0.00 4.79
3296 3947 1.877443 GGCTGAAAACCTGAGCGTTTA 59.123 47.619 0.64 0.00 34.89 2.01
3297 3948 2.292292 GGCTGAAAACCTGAGCGTTTAA 59.708 45.455 0.64 0.00 34.89 1.52
3303 3954 5.751028 TGAAAACCTGAGCGTTTAAATTTGG 59.249 36.000 0.00 0.00 34.89 3.28
3312 3963 7.846485 TGAGCGTTTAAATTTGGTTGAAATTC 58.154 30.769 0.00 0.00 42.41 2.17
3323 3985 4.651778 TGGTTGAAATTCTAGGTCAGGTG 58.348 43.478 0.00 0.00 0.00 4.00
3325 3987 5.070685 GGTTGAAATTCTAGGTCAGGTGTT 58.929 41.667 0.00 0.00 0.00 3.32
3326 3988 5.535030 GGTTGAAATTCTAGGTCAGGTGTTT 59.465 40.000 0.00 0.00 0.00 2.83
3327 3989 6.040504 GGTTGAAATTCTAGGTCAGGTGTTTT 59.959 38.462 0.00 0.00 0.00 2.43
3328 3990 7.229907 GGTTGAAATTCTAGGTCAGGTGTTTTA 59.770 37.037 0.00 0.00 0.00 1.52
3329 3991 8.626526 GTTGAAATTCTAGGTCAGGTGTTTTAA 58.373 33.333 0.00 0.00 0.00 1.52
3355 4022 8.854979 TTTACTGAATTTTCATCATATTGGCG 57.145 30.769 0.00 0.00 36.46 5.69
3371 4039 4.681074 TTGGCGTGATAGGATACATCAA 57.319 40.909 0.00 0.00 34.32 2.57
3375 4043 3.859961 GCGTGATAGGATACATCAATCGG 59.140 47.826 0.00 0.00 34.32 4.18
3378 4046 6.156519 CGTGATAGGATACATCAATCGGAAA 58.843 40.000 0.00 0.00 34.32 3.13
3379 4047 6.645003 CGTGATAGGATACATCAATCGGAAAA 59.355 38.462 0.00 0.00 34.32 2.29
3535 4203 8.960591 AGATGAATTATTTAACCCTTGTCTGTG 58.039 33.333 0.00 0.00 0.00 3.66
3655 4327 4.894784 TGGTACTTCTAAACAGAAGGCAG 58.105 43.478 16.48 0.00 46.93 4.85
3762 4449 1.835483 CGACAGTTGACAGTGCAGGC 61.835 60.000 0.00 0.00 0.00 4.85
3765 4452 1.301244 AGTTGACAGTGCAGGCGAG 60.301 57.895 0.00 0.00 0.00 5.03
3787 4474 6.508563 CGAGTAACATATGCTGACATGTGAAC 60.509 42.308 1.15 0.00 45.48 3.18
3804 4491 5.826586 TGTGAACGTCAAACTGCATATTTT 58.173 33.333 0.00 0.00 0.00 1.82
3833 4520 7.962441 AGGTACAAAAATGTAGCCTGAAAAAT 58.038 30.769 12.93 0.00 41.98 1.82
3945 4632 2.400408 CGTGTCAAAAAGGCGAAATTCG 59.600 45.455 11.47 11.47 43.89 3.34
3955 4642 1.673920 GGCGAAATTCGGGCAAATAGA 59.326 47.619 17.49 0.00 40.84 1.98
3960 4647 4.970003 CGAAATTCGGGCAAATAGATTGTC 59.030 41.667 7.61 0.00 43.10 3.18
3967 4654 4.876107 CGGGCAAATAGATTGTCTACAAGT 59.124 41.667 1.62 0.00 43.36 3.16
4028 4715 9.090103 AGTATCCTTAATGATAAGTGATCCGAA 57.910 33.333 2.44 0.00 37.42 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 1.070786 GAGTTGCCCGGTCTGTGAA 59.929 57.895 0.00 0.00 0.00 3.18
75 76 0.250338 AAAGAGTGAGTTGCCCGGTC 60.250 55.000 0.00 0.00 0.00 4.79
79 80 3.542648 GGGTATAAAGAGTGAGTTGCCC 58.457 50.000 0.00 0.00 0.00 5.36
85 86 5.693769 TGAAAGGGGGTATAAAGAGTGAG 57.306 43.478 0.00 0.00 0.00 3.51
86 87 6.243148 GTTTGAAAGGGGGTATAAAGAGTGA 58.757 40.000 0.00 0.00 0.00 3.41
105 106 2.904866 GCACCACAGCCCGTTTGA 60.905 61.111 0.00 0.00 0.00 2.69
106 107 2.906897 AGCACCACAGCCCGTTTG 60.907 61.111 0.00 0.00 34.23 2.93
107 108 2.594592 GAGCACCACAGCCCGTTT 60.595 61.111 0.00 0.00 34.23 3.60
108 109 3.414136 TTGAGCACCACAGCCCGTT 62.414 57.895 0.00 0.00 34.23 4.44
109 110 3.832237 CTTGAGCACCACAGCCCGT 62.832 63.158 0.00 0.00 34.23 5.28
110 111 3.052082 CTTGAGCACCACAGCCCG 61.052 66.667 0.00 0.00 34.23 6.13
111 112 3.368571 GCTTGAGCACCACAGCCC 61.369 66.667 0.00 0.00 41.59 5.19
133 134 0.951558 GCTTTTCTTTCCAGCGGTGA 59.048 50.000 17.83 0.00 0.00 4.02
134 135 0.039165 GGCTTTTCTTTCCAGCGGTG 60.039 55.000 7.86 7.86 34.09 4.94
166 169 3.970410 CAGCAAGGAGGTGGGGCA 61.970 66.667 0.00 0.00 41.98 5.36
168 171 1.303643 GTTCAGCAAGGAGGTGGGG 60.304 63.158 0.00 0.00 45.66 4.96
170 173 0.607489 CCTGTTCAGCAAGGAGGTGG 60.607 60.000 0.00 0.00 45.66 4.61
198 201 3.376859 TCAACACTCGACAACAGCATTTT 59.623 39.130 0.00 0.00 0.00 1.82
212 216 2.740714 GCCGTGCCGATCAACACTC 61.741 63.158 11.95 2.41 34.58 3.51
213 217 2.742372 GCCGTGCCGATCAACACT 60.742 61.111 11.95 0.00 34.58 3.55
214 218 4.147322 CGCCGTGCCGATCAACAC 62.147 66.667 5.26 5.26 0.00 3.32
297 302 9.679661 AACAATGGAGTATAATCACATGTTACA 57.320 29.630 12.16 0.00 0.00 2.41
469 474 5.406649 TGGTTAAACACAAGTTTTGCAGAG 58.593 37.500 0.00 0.00 45.32 3.35
474 479 7.971168 TGTCAGTATGGTTAAACACAAGTTTTG 59.029 33.333 0.00 0.00 40.12 2.44
535 545 5.917447 GCTGAAAGAAAAACTGGAGAATGAC 59.083 40.000 0.00 0.00 34.07 3.06
591 601 3.195396 CACTTCACCATTACAAATGGGGG 59.805 47.826 18.44 11.97 42.75 5.40
611 622 1.102978 ATTACTGGAAATGGCGCCAC 58.897 50.000 35.50 20.34 0.00 5.01
692 703 1.626654 ATTCCACGCGAAACAGCTCG 61.627 55.000 15.93 0.00 41.84 5.03
693 704 0.095417 GATTCCACGCGAAACAGCTC 59.905 55.000 15.93 0.00 33.08 4.09
694 705 0.320771 AGATTCCACGCGAAACAGCT 60.321 50.000 15.93 0.00 33.08 4.24
695 706 0.179215 CAGATTCCACGCGAAACAGC 60.179 55.000 15.93 0.00 33.08 4.40
696 707 1.136252 CACAGATTCCACGCGAAACAG 60.136 52.381 15.93 0.00 33.08 3.16
697 708 0.865111 CACAGATTCCACGCGAAACA 59.135 50.000 15.93 0.00 33.08 2.83
698 709 0.452784 GCACAGATTCCACGCGAAAC 60.453 55.000 15.93 0.00 33.08 2.78
699 710 1.573829 GGCACAGATTCCACGCGAAA 61.574 55.000 15.93 4.20 33.08 3.46
700 711 2.032634 GGCACAGATTCCACGCGAA 61.033 57.895 15.93 0.00 34.14 4.70
701 712 2.434185 GGCACAGATTCCACGCGA 60.434 61.111 15.93 0.00 0.00 5.87
702 713 3.853330 CGGCACAGATTCCACGCG 61.853 66.667 3.53 3.53 0.00 6.01
759 770 0.390472 CCAGACCACCGAGCTCTTTC 60.390 60.000 12.85 0.74 0.00 2.62
875 899 3.615110 GCGAGAGAGATTGTTTGGTCTGA 60.615 47.826 0.00 0.00 0.00 3.27
910 934 0.746563 TTCCATGGACGAAATCGCCC 60.747 55.000 15.91 0.83 44.43 6.13
942 966 0.464373 GCGAATCAGGGAAGATGGCA 60.464 55.000 0.00 0.00 31.99 4.92
943 967 0.179034 AGCGAATCAGGGAAGATGGC 60.179 55.000 0.00 0.00 0.00 4.40
948 972 1.884926 GGCGAGCGAATCAGGGAAG 60.885 63.158 0.00 0.00 0.00 3.46
971 995 1.611519 TTGGTTGGGTTTAAGGCGAG 58.388 50.000 0.00 0.00 0.00 5.03
972 996 2.164338 GATTGGTTGGGTTTAAGGCGA 58.836 47.619 0.00 0.00 0.00 5.54
973 997 1.203758 GGATTGGTTGGGTTTAAGGCG 59.796 52.381 0.00 0.00 0.00 5.52
974 998 1.553248 GGGATTGGTTGGGTTTAAGGC 59.447 52.381 0.00 0.00 0.00 4.35
975 999 2.896039 TGGGATTGGTTGGGTTTAAGG 58.104 47.619 0.00 0.00 0.00 2.69
1110 1140 1.752833 GGGCCGGGAGTATCGATTT 59.247 57.895 1.71 0.00 34.37 2.17
1247 1280 2.415010 CAGCGACCTCCATCTCGG 59.585 66.667 0.00 0.00 0.00 4.63
1438 1480 2.234908 AGAGGTTGAACAGAATCGAGGG 59.765 50.000 0.00 0.00 0.00 4.30
1464 1506 0.105658 TGGAGTCGGGAGGGATTAGG 60.106 60.000 0.00 0.00 0.00 2.69
1469 1511 2.041922 CCATGGAGTCGGGAGGGA 60.042 66.667 5.56 0.00 0.00 4.20
1523 1888 1.320382 CGTGCGCGTTGTTGATGAAC 61.320 55.000 12.43 0.00 0.00 3.18
1625 1990 0.107993 CGATGAAGAGCTTGGGCAGA 60.108 55.000 0.00 0.00 41.70 4.26
1964 2330 0.034616 AGGAGTCAGACAAGCAGCAC 59.965 55.000 2.66 0.00 0.00 4.40
2076 2449 1.909700 TCCAAGCATTCCCACAGAAC 58.090 50.000 0.00 0.00 37.29 3.01
2084 2457 5.841957 AATTAGACACATCCAAGCATTCC 57.158 39.130 0.00 0.00 0.00 3.01
2147 2524 8.754991 TCAAAAGACCTGAAAACTTAATACCA 57.245 30.769 0.00 0.00 0.00 3.25
2165 2784 2.957402 ACAGCTCCACCATCAAAAGA 57.043 45.000 0.00 0.00 0.00 2.52
2175 2794 4.184629 CCTACATAGTCAAACAGCTCCAC 58.815 47.826 0.00 0.00 0.00 4.02
2241 2860 4.706962 CCTTCAGGGTTCCCTTCTTTAATG 59.293 45.833 7.79 0.00 33.50 1.90
2404 3023 5.874897 AATTTGCATTGTACAGGGCATAT 57.125 34.783 19.95 17.70 35.98 1.78
2540 3180 0.878523 TCGACCCACAGCGTGAAAAG 60.879 55.000 9.75 0.93 35.23 2.27
2555 3196 4.793216 GCAAATATGTCACACCAAATCGAC 59.207 41.667 0.00 0.00 0.00 4.20
2577 3218 2.672874 TCGCTGTACAATGACATGAAGC 59.327 45.455 0.00 0.00 0.00 3.86
2641 3282 1.648467 GCAGCTAAAAGCCCACGGAG 61.648 60.000 0.00 0.00 43.77 4.63
2644 3285 1.378531 TATGCAGCTAAAAGCCCACG 58.621 50.000 0.00 0.00 43.77 4.94
2649 3290 6.037610 ACAGAACAGTATATGCAGCTAAAAGC 59.962 38.462 0.00 0.00 42.84 3.51
2716 3358 2.481952 GCAGCCAGAACTTTCTACACAG 59.518 50.000 0.00 0.00 35.34 3.66
2718 3360 2.739379 GAGCAGCCAGAACTTTCTACAC 59.261 50.000 0.00 0.00 35.34 2.90
2721 3363 3.603532 CATGAGCAGCCAGAACTTTCTA 58.396 45.455 0.00 0.00 35.34 2.10
2768 3410 1.357137 TGGGGAACACAGCATGAGTA 58.643 50.000 0.00 0.00 39.59 2.59
2890 3533 0.610509 TGGCCCAGCTGCGATAAAAA 60.611 50.000 8.66 0.00 0.00 1.94
3081 3726 1.172180 TTTGTTTCGCTGGAGCTGGG 61.172 55.000 0.00 0.00 39.32 4.45
3209 3854 4.572389 ACAGCATTAGAAGCGAAATACAGG 59.428 41.667 0.00 0.00 37.01 4.00
3217 3862 2.223502 CGGTCTACAGCATTAGAAGCGA 60.224 50.000 0.00 0.00 37.01 4.93
3242 3887 5.856455 GTCATGTCAGGAAATTAAAACACCG 59.144 40.000 0.00 0.00 0.00 4.94
3243 3888 6.744112 TGTCATGTCAGGAAATTAAAACACC 58.256 36.000 0.00 0.00 0.00 4.16
3272 3922 1.609208 GCTCAGGTTTTCAGCCTTCA 58.391 50.000 0.00 0.00 33.31 3.02
3296 3947 7.290014 ACCTGACCTAGAATTTCAACCAAATTT 59.710 33.333 0.00 0.00 43.56 1.82
3297 3948 6.782494 ACCTGACCTAGAATTTCAACCAAATT 59.218 34.615 0.00 0.00 45.76 1.82
3303 3954 6.635030 AAACACCTGACCTAGAATTTCAAC 57.365 37.500 0.00 0.00 0.00 3.18
3312 3963 8.842358 TCAGTAAATTAAAACACCTGACCTAG 57.158 34.615 0.00 0.00 0.00 3.02
3329 3991 9.467258 CGCCAATATGATGAAAATTCAGTAAAT 57.533 29.630 1.98 0.00 41.08 1.40
3355 4022 7.962964 TTTTCCGATTGATGTATCCTATCAC 57.037 36.000 0.00 0.00 34.50 3.06
3464 4132 3.428045 CGATTCCTTGGAAACATTGCTCC 60.428 47.826 6.16 0.00 42.32 4.70
3530 4198 2.343758 GAGCTTGGACCGCACAGA 59.656 61.111 0.00 0.00 0.00 3.41
3535 4203 2.435059 GACTGGAGCTTGGACCGC 60.435 66.667 0.00 0.00 0.00 5.68
3655 4327 2.550487 TGTGTCCATTACGCAAGCC 58.450 52.632 0.00 0.00 45.44 4.35
3665 4337 4.012374 CCAGCTAAGTTCAATGTGTCCAT 58.988 43.478 0.00 0.00 0.00 3.41
3743 4430 1.835483 GCCTGCACTGTCAACTGTCG 61.835 60.000 0.00 0.00 0.00 4.35
3762 4449 5.043248 TCACATGTCAGCATATGTTACTCG 58.957 41.667 4.29 0.00 35.46 4.18
3765 4452 5.063438 ACGTTCACATGTCAGCATATGTTAC 59.937 40.000 4.29 1.32 35.46 2.50
3787 4474 5.920273 ACCTTCAAAAATATGCAGTTTGACG 59.080 36.000 13.91 12.55 40.11 4.35
3804 4491 6.065374 TCAGGCTACATTTTTGTACCTTCAA 58.935 36.000 0.00 0.00 0.00 2.69
3833 4520 4.568072 AAGTGTGTATATGCAGACCCAA 57.432 40.909 15.89 0.00 33.71 4.12
3925 4612 2.724174 CCGAATTTCGCCTTTTTGACAC 59.276 45.455 13.26 0.00 38.82 3.67
3945 4632 6.759497 AACTTGTAGACAATCTATTTGCCC 57.241 37.500 0.00 0.00 39.03 5.36
3973 4660 8.646900 GGCAATTACCCCATATTTGAGATTTTA 58.353 33.333 0.00 0.00 0.00 1.52
3975 4662 6.043127 GGGCAATTACCCCATATTTGAGATTT 59.957 38.462 1.70 0.00 45.00 2.17


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.